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ORCIDAndreas Dräger
Person information
- affiliation: University of Tübingen, Center for Bioinformatics (ZBIT), Germany
- affiliation: University of California, San Diego, Department of Bioengineering, CA, USA
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Books and Theses
- 2011
[b1]Andreas Dräger:
Computational Modeling of Biochemical Networks. Eberhard Karls University of Tübingen, 2011, ISBN 978-3-86853-850-2, pp. 1-254
Journal Articles
- 2023
- [j44]Manuel Glöckler
, Andreas Dräger, Reihaneh Mostolizadeh:
Hierarchical modelling of microbial communities. Bioinform. 39(1) (2023) - [j43]Bhanwar Lal Puniya, Andreas Dräger:
Advancements in computational modelling of biological systems: seventh annual SysMod meeting. Bioinform. 39(9) (2023) - [j42]Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, Andreas Dräger:
Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. Frontiers Bioinform. 3 (2023) - [j41]Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, Andreas Dräger:
New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells. PLoS Comput. Biol. 19(3) (2023) - 2022
- [j40]Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, Andreas Dräger:
The systems biology simulation core library. Bioinform. 38(3): 864-865 (2022) - [j39]Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger:
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. 38(21): 4990-4993 (2022) - [j38]Constantin Holzapfel, Miriam Hoene, Xinjie Zhao, Chunxiu Hu, Cora Weigert, Andreas Niess, Guowang Xu, Rainer Lehmann, Andreas Dräger, Michael Krone:
FluxomicsExplorer: Differential visual analysis of Flux Sampling based on Metabolomics. Comput. Graph. 108: 11-21 (2022) - [j37]Manuel Glöckler, Andreas Dräger, Reihaneh Mostolizadeh:
NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome. Frontiers Bioinform. 2: 827024 (2022) - 2021
- [j36]Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar:
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37(21): 3702-3706 (2021) - 2020
- [j35]Alina Renz, Lina Widerspick, Andreas Dräger:
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2. Bioinform. 36(Supplement-2): i813-i821 (2020) - [j34]Lea Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Ottar Rolfsson, Julian Heinrich, Andreas Dräger:
Visualizing metabolic network dynamics through time-series metabolomic data. BMC Bioinform. 21(1): 130 (2020) - [j33]Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna:
Systems biology graphical notation markup language (SBGNML) version 0.3. J. Integr. Bioinform. 17(2-3) (2020) - [j32]Fengkai Zhang, Lucian P. Smith, Michael L. Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia, Sarah M. Keating, Nicolas Rodriguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim:
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J. Integr. Bioinform. 17(2-3) (2020) - [j31]Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, Zachary A. King:
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res. 48(Database-Issue): D402-D406 (2020) - 2019
- [j30]Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - [j29]Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, Alfonso Urso:
The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. BMC Bioinform. 20-S(4): 125:1-125:9 (2019) - [j28]Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019) - [j27]Adrien Rougny, Vasundra Touré, Stuart L. Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Ugur Dogrusoz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly A. Sorokin, Falk Schreiber, Augustin Luna:
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j26]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018) - [j25]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018) - 2016
- [j24]Bin Du, Daniel C. Zielinski, Erol S. Kavvas, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla E. Ruggiero, Garri A. Arzumanyan, Bernhard O. Palsson:
Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst. Biol. 10: 40 (2016) - [j23]Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis:
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 44(Database-Issue): 515-522 (2016) - [j22]Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger:
Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling. PLoS Comput. Biol. 12(1) (2016) - 2015
- [j21]Nicolas Rodriguez, Alex Thomas, Leandro H. Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger:
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinform. 31(20): 3383-3386 (2015) - [j20]Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, Andreas Zell:
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst. Biol. 9: 68 (2015) - [j19]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015) - [j18]Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson:
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput. Biol. 11(8) (2015) - 2014
- [j17]Alexander Dörr, Roland Keller, Andreas Zell, Andreas Dräger:
SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology. Comput. 2(4): 246-257 (2014) - 2013
- [j16]Sebastian Vlaic, Bianca Hoffmann, Peter Kupfer, Michael Weber, Andreas Dräger:
GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinform. 29(17): 2216-2217 (2013) - [j15]Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell:
Precise generation of systems biology models from KEGG pathways. BMC Syst. Biol. 7: 15 (2013) - [j14]Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard R. Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger:
The systems biology simulation core algorithm. BMC Syst. Biol. 7: 55 (2013) - [j13]Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère:
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7: 116 (2013) - [j12]Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan M. Kowal, Benjamin Wicks, Emanuel J. V. Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez, Tomás Helikar:
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst. Biol. 7: 135 (2013) - 2012
- [j11]Matthias König, Andreas Dräger, Hermann-Georg Holzhütter:
CySBML: a Cytoscape plugin for SBML. Bioinform. 28(18): 2402-2403 (2012) - [j10]Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Johannes Eichner, Nicolas Rodriguez, Nicolas Le Novère, Andreas Zell:
Qualitative translation of relations from BioPAX to SBML qual. Bioinform. 28(20): 2648-2653 (2012) - 2011
- [j9]Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, Michael Hucka:
JSBML: a flexible Java library for working with SBML. Bioinform. 27(15): 2167-2168 (2011) - [j8]Clemens Wrzodek, Andreas Dräger, Andreas Zell:
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinform. 27(16): 2314-2315 (2011) - [j7]Adrian Schröder, Johannes Wollnik, Clemens Wrzodek, Andreas Dräger, Michael Bonin, Oliver Burk, Maria Thomas, Wolfgang E. Thasler, Ulrich M. Zanger, Andreas Zell:
Inferring statin-induced gene regulatory relationships in primary human hepatocytes. Bioinform. 27(18): 2473-2477 (2011) - 2010
- [j6]Clemens Wrzodek, Adrian Schröder, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, Marcel Kronfeld, Klaus Harter, Andreas Zell:
ModuleMaster: A new tool to decipher transcriptional regulatory networks. Biosyst. 99(1): 79-81 (2010) - 2009
- [j5]Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, Andreas Zell:
SBML2LATEX: Conversion of SBML files into human-readable reports. Bioinform. 25(11): 1455-1456 (2009) - [j4]Andreas Dräger, Marcel Kronfeld, Michael J. Ziller, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Oliver Kohlbacher, Andreas Zell:
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst. Biol. 3: 5 (2009) - [j3]Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, Andreas Zell:
BowTieBuilder: modeling signal transduction pathways. BMC Syst. Biol. 3: 67 (2009) - 2008
- [j2]Richard C. G. Holland, Thomas A. Down, Matthew R. Pocock, Andreas Prlic, David S. Huen, Keith James, Sylvain Foisy, Andreas Dräger, Andy Yates, Michael L. Heuer, Mark J. Schreiber:
BioJava: an open-source framework for bioinformatics. Bioinform. 24(18): 2096-2097 (2008) - [j1]Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, Andreas Zell:
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst. Biol. 2: 39 (2008)
Conference and Workshop Papers
- 2020
- [c7]Michael Krone, Andreas Dräger, Ebru Cobanoglu, Manuel Otto Harke, Miriam Hoene, Cora Weigert, Rainer Lehmann:
A Web-based Visual Analytics Application for Biological Networks. EuroVis (Posters) 2020: 41-43 - 2011
- [c6]Adrian Schröder, Clemens Wrzodek, Johannes Wollnik, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, Andreas Zell:
Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization. IEEE Congress on Evolutionary Computation 2011: 2285-2292 - 2010
- [c5]Sandro Lambeck, Andreas Dräger, Reinhard Guthke:
Network Inference by Considering Multiple Objectives: Insights from In Vivo Transcriptomic Data Generated by a Synthetic Network. BIOCOMP 2010: 734-742 - 2009
- [c4]Marcel Kronfeld, Andreas Dräger, Moritz Aschoff, Andreas Zell:
On the Benefits of Multimodal Optimization for Metablic Network Modeling. GCB 2009: 191-200 - 2007
- [c3]Jochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger, Andreas Zell:
Inferring Gene Regulatory Networks by Machine Learning Methods. APBC 2007: 247-256 - [c2]Andreas Dräger, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Andreas Zell:
Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum. IEEE Congress on Evolutionary Computation 2007: 620-627 - [c1]Andreas Dräger, Marcel Kronfeld, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Andreas Zell:
Benchmarking evolutionary algorithms on convenience kinetics modelsof the valine and leucine biosynthesis in C. glutamicum. IEEE Congress on Evolutionary Computation 2007: 896-903
Coauthor Index
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